Guilt of the Innocent
by Dark Angel's Blue Fire
Summary: When an old enemy from Jim's past surfaces Jim puts everything on the line to protect his crew and his bond-mate. Only to have his world shatter around him. Now he is Captain no more and with Bones in tow, is chasing the ghosts of his past to protect his future. Meanwhile Spock slowly realises the mistakes he made. Will he get to Jim before it's too late? Jim/Spock


This is what happens when you stumble onto a new fandom. You become obsessed with it. So now here I am after reading some rather awesome Star Trek fanfics trying my hand at writing them myself. Okay so before we go any further **THIS IS SLASH of the Jim/Spock **variety. If you don't like please don't read. Also, there is angst galore in this. And Im sorry if something that resembles a super Jim and Bones has appeared, I found them that way. I love them that way :D.

There will be **dark themes **running through this story but I will put warnings on each chapter that deal with them.

I do not, of course own Star Trek. I do wish, but no. It's not mine. I wish I owned Jim but then Spock might just try and kill me. So I'll leave him alone. For now. :D

Okay I've babbled enough.

Without anything further to day I give you... Guilt of the Innocent.

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Guilt Of The Innocent

Prologue: Blood and Shadows

The Planet of VIII lay so perilously close to the boarder of the neutral zone that navigation charts differ on it's placement. Some put it on the side of the Neutral Zone while others said it fell into Federation manned space. Despite its dubious placement the tiny planet hardly achieved a customary glance on a star chart by either side of the boarder. It had little to offer either side and was left alone.

It was simply vast expanses of jungle with wild creatures and sentient trees that took offence at people trying to chop them down. The indigenous peoples were wild but there respect of their planet and the animals they lived along side, was something that boarded on reverence.

They had little use for outsiders and although Federation Starships had been to their planet before they were content to continue their life as it had always been. They were a people of tribe law and masters of their planet. Dangerous and deadly with little use for outsiders so they had been left to their own devices and thrived on their wild planet.

It was a great planet for someone wanting to hide. For someone that knew nowhere in Federation space was safe. High in the tree tops of the jungle canopy there is a small discreet tree house. The house cannot be seen from the ground, great pains have been made to make sure of that. It has all the facilities a person could want. It is a house in paradise. It is a self imposed prison, a gilded cage for someone who is hiding. Hiding for their life.

The twin moons of the planet cast an eerie but beautiful glow over the planet. In the tree tops all was quiet, the canopy usually so full of life was quiet. The animals that make their life during the day are sleeping, the jungle was quiet for the night. The hidden tree house is silent along with it.

Then the door moves, it's subtle, a faint rattling, then as suddenly the door stops moving. The man inside the room lifted his head to listen. His eyes were instantly wide and alert as he cranes his senses to work out what has happened. The door is sturdy made from the wood of the native trees. He had to work with them for over a month before they would share their bark, share their protection with him. But they were gentle and understanding of his plight so they shared their strength with him. His house would be strong enough to withstand a grenade blast. The wind would not have moved it. At least, not like that. The door would not move on his own, of that he is sure. He made his house that way.

The man is out of his hammock now, Eyes intense, His hazel eyes are more intense than any humans almost glowing in the night. All his senses were suddenly on alert. He could feel something, something that was different from the normal movements in the jungle.

He ducks suddenly as a blast from a weapon that is widely unused in Federation space erupts through the wall. He avoided the shattering would but his head explodes with the pain the tree was in. He couldn't think of that then though. There was no time. He picks up the weapon, a lot like a phaser that he has kept hidden always within his reach inside his house.

From a crouched position, low to the ground, he returned fire quickly through the whole in the wall. His hearing picks up a faint gasp somewhere in the jungle telling him that he had scored a hit but he doesn't wait to find out how well a hit. He dives out of the little window and into the canopy of the surrounding jungle as if the fortified wood he made his house with were paper. His tree lets him go easily trying to help him get away.

_Logan, _voices say in his head. _Run, don't look back, run!_

Logan, for that is his name, runs quickly across the top of the branches knowing that they are behind him, but he hopes knowing this jungle as he does will help. He swings from branch to branch with sure movements moving along the branches like a child in a jungle gym. But he knows that they could catch him. They have the same skills he does but he has to hope he can make it out of there. He has a plan, he has a transport hidden about a mile left of his present location for exactly this reason. He just has to get to it. He thinks he's made it, He's a metre from where he hid the transport, he's a metre from freedom, but then he hits a wall.

He stumbles backwards disorientated for a moment there's nothing there, but then the wall picks him up and a huge man appears with mousy hair and black eyes and a snarl on his face. Logan closes his eyes. For a moment he feels defeated and lost. They've found him.

All that hiding and they found him. It had all been for nothing. But the game wasn't over yet. He still had time. He still had a chance.

"Well, well, well what do we have here?" A voice said, a tall slim shadow coming round the brute that held him captive. "A Slayer caught off guard? You've let your training slip Logan, that was so easy it's pathetic."

Logan narrowed his eyes, fear being replaced by anger in his hazel eyes. "You lost the right to call me that a long time ago." "Oh and what would you have me call you Incubus? Please the time of playing children's games is over." Logan smirked, "Call me _Number one, _That is what my designation is after all. There was a snarl from the second man who was still encased in shadows he stepped out into the moonlight to get into Logan's face.

"Number One is my designation _mine. _And after I'm through with you there will be only one." Logan laughed. "Right. Because that ever made a difference. Face it _Aaron," _Logan spat the name as if it were something poisonous, "You'll never be good enough. You never were. It was always _Him. _He took everything that was thrown at him and was always the favourite and he always will be." The punch was quick and hard.

Pain exploded down Logan's face as he felt his nose break and blood began to run from the injury. But he didn't even whimper. He'd had worse. Aaron stalked towards him where he was still held in place by the silent man who now slammed him against a tree trunk with enough force to crack it. "Listen to me you self righteous prick. You're going to tell me where they are."

Logan laughed then. "No. I'm not. I don't know where they are, and even if I did I wouldn't be telling you." Aaron snarled, "Yes you will. One way or another you will tell me. How painful it becomes is up to you. You will tell me and then my dear _brother, _you will Will me your power."

Logan's eyes went hard. "No."

Aaron smiled. "We shall see." He stepped right up to Logan his sliver eyes glowing, "Tell me where they are." Logan narrowed his eyes feeling Aarons power push against his shields. "No." He said and then threw some of his own power at the man holding him captive. The man gasped doubling over and Logan was released. He fell to the floor and was up quicker than the eye could follow.

Aaron was quicker though. "Feisty today aren't we Logan? What happened to the _we don't have to fight _manta you used to spout?" "You don't apply. You are the exception to my rule. I will regret the day I didn't kill you. Always." Logan said lashing out again. This time he caught Aaron and Aaron doubled over, all the pain of a past gone by, relived. Logan snarled and launched himself at Aaron and they tumbled through the trees further than any human could survive and their crash to the ground was deafening.

Logan had managed to land on top of Aaron and slammed him into the ground again. "Why are you still with _him." _Logan snarled. "Why? After everything he did to us on that rock?" "I am his favoured. He will reward me for being loyal." For a moment Logan felt for Aaron he would never learn. He would never understand. But Logan wanted him too. He wished Aaron could see.

"You're delusional." Logan said his eyes wide. "You should have never left." Aaron said his eyes showing compassion for a moment. I could have spoken to him for you. But now you're a escapee you know he doesn't tolerate that. I have to take you in."

"I'd rather die." Logan snapped his eyes burning hazel fire. Aaron's features became hard again. "That can be arranged." Then without warning Aaron attacked Logan smashing through his shields as if they were paper and Logan knew he had been tricked. After all this time he'd still, even for a minute, believed the best in his once brother. Now that moment would kill him.

Logan's mind flooded with images he tried to tell himself weren't real, knew they weren't real. But it didn't matter. His mind was captured in the web of lies. And he would die in it. Aarons power flooded his mind it didn't matter he'd known it wasn't real he was back in hell. On that god forsaken rock with no way out. He tried to fight it but his will power was crushed under the weight of Aarons power.

He was trapped in a cage from so long ago tied to a pyre but this time instead of JT breaking them out he knew he would die. He was choking on smoke feel the flames burning him alive. He screamed. The pain was worse than he remembered. He knew he would die. _Will Aaron, will Havoc your power..._ He almost did it to end the pain then he remembered his brothers and sisters. And the small part of him that wanted to fight even though it seemed pointless remembered something. Remembered Aaron. And he recoiled from giving his power to him.

The part of himself that was defiant even in death screamed out his last battle. He could not let them have his power. He summoned up the last of his strength even as the flames climbed higher and clawed a symbol into his skin. A jaggered star with a lightening bolt underneath. He pressed it feeling it burn. Feeling the agony as his power was ripped from it. "I will my power to Maverick. JT, My brother, my friend my power and all I have is yours brother. They are coming." He felt his power flow from him and he drifted away the pain gone. And he was thankful for it.

Aaron stood and watched impassively as Logan writhed on the floor of the jungle caught in a nightmare of Aaron's making. But Aaron continued to watch as Logan screamed. He was waiting. Any minute now, He smiled as Logan's arm started to burn the crudely made tattoo lightning up in the dark jungle. "Come on Logan. He pressed into Logan's thoughts _will me your power._

For a moment it almost seemed to have worked and then Logan whispered, "My power to Maverick." Aaron screamed as Logan's tattoo burned blue and then light burst into the sky. Then Logan took his last breath.

Aaron screamed again in anger his eyes glowing in the dark. There was a noise and Carter, the one that had held Logan captive appeared beside Aaron. "What happened?" Carter looked down at Logan. "You killed him!" Aaron rounded on his companion his eyes burned for a moment and said, "I did no such thing he fell from the trees when he refused to come back home. He betrayed us." Carter looked dazed for a moment and then his eyes cleared and his eyes hardened. "Traitor. How could he?"

"I don't know," Aaron looked to the sky "Come on there is much to do and I have to report back to the Boss. Hopefully the others will be more responsive."

They made their way back through the jungle and left the planet as if they'd never been there to begin with.

At the other side of the Galaxy Captain Jim Kirk stifled a scream as he woke from a particularly vivid nightmare. He stumbled from the bed pleased, for once, that his lover was on Gamma shift this week. He got himself to the bathroom where he was violently sick. Once he was done he cleaned himself up and looked in the mirror, what he saw horrified him.

His eyes, the blue that had always been his brand, were glowing in the dark. Jim closed his eyes. "No." "Oh no." He whispered. The grief almost crippled him and then he felt the burn he knew was coming and looked down at his right arm. A crude symbol of a star with a lightening bolt under it appeared but it was the words, in a language Jim had tried to forget, appearing on his skin that horrified him. "_My power is yours brother. They are coming." _

He launched himself for the communicator and managed to gasp, "Bones," into it before the pain came and he collapsed into the bathroom on a scream. He vaguely heard the door burst open and his lover's voice calling for him, He heard Bones shouting instructions, but he could do nothing for the pain. His eyes were caught on the tattoo that was slowly disappearing, and as he lost his battle with the black abyss pulling him into a world of nothing, he knew that everything was about to change.

**96 hours Later...**

Captain James Tiberius Kirk stood regulation perfect in front of the three Admirals that had called him home. His facial expression was neutral as he regarded his commanders but his eyes snapped blue fire. "So what your telling me Sir," He said softly. "Is that it failed. They escaped." Outwardly Jim appeared calm but the men in the room knew better than to think Jim was calm. Jim's eyes fell on Admiral Christopher Pike and was gratified to see at least, the same anger in his mentor's eyes.

"Yes Jim." He said softly. "I'm sorry. They're free. They got away from us. We've got a unit tracking them now." Jim laughed but it was bitter. "You'll never catch them. This is what they do. I warned you, I told you what they were capable of." He looked at the others. "How did they even escape? I locked them in Black Out myself. Trust me I made sure they weren't leaving."

Admiral John Archer pulled a hand across his face. "We think they had inside help." Jim's eyes narrowed. "They what?" "We're investigating Jim," Archer said but until we find something worth anything we're stuck."

Jim regarded the Admirals in front of him. The three Admirals that had actually believed he was worth something, who even after everything still believed he was better than dirt. The people who thought that of him were in short supply these days.

Jim looked at the ceiling for a moment and made his decision. There was no choice really, if they were free he had to think of those he had to protect. And he couldn't go back. Not now. His time as Captain was over, but he could still be the best commander he could be. He had to be. There were people relying on him to keep them safe. Now he had to think of them.

That task had never seemed so impossible but if there was something Jim Kirk was good at doing, he was good at overcoming the impossible. There was a reason he didn't believe in no-win scenarios. He'd survived one.

"You'll never catch them, and you'll never find out who helped them. Not without my help." He said finally making his decision heard. He saw Chris close his eyes for a moment.

"I know how they work, how they operate. Their mistakes are few but they do make them. Let me put a team together. Let me hunt them down. Let me be there when they make a mistake, let me catch them. Let me make sure nothing like this ever happens again."

"Jim..." Admiral Barnett said softly, Jim glanced at him and Jim saw the despair flitter across all three Admiral's faces. "What about the Enterprise?" Now Jim had to close his eyes against the sudden ambush of emotion. "Give Commander Spock command of the Enterprise. I resign as her Captain." "I had assumed if you made this team Commander Spock would be your second." Chris said softly. "No. Commander Spock made his opinions of me and my command style quite clear during and in the aftermath of this mission. Leave him on the Enterprise in command. It's what he wants."

"Jim... Are you sure what about your..." "He made himself quite clear." Jim cut across Chris his eyes flashing. "I won't force him to see something he has no wish to see." Jim looked intently at the three admirals. The only people in Starfleet fully in the loop.

"You need me to catch them. You know you can't do it alone. And no one else can track them like I can. I have the others to think about too. They already killed Logan. I won't let them do it again. My time as Captain is over."

At that moment the door to the conference room was flung open and Jim was hit by a blue hurricane. A snarling blue hurricane. "God damnit Jim!" A southern accent snarled. "I told you not to move until I'd looked you over. I knew I should have hand cuffed you to the bio bed Let me see it!"

Before Jim could say anything his shirt was being lifted up and away from his body and being gently probed by professional but gentle touches. "God Damnit Jim! What possessed you to move from sick bay how are you even standing up! You could have bled out!" Before he can protest there are a number of quick fire hypo sprays into his neck and the constant dull ache that Jim had grown accustomed too disappeared.

The hurricane that had accosted him had a name. His name was Dr. Leonard "Bones" McCoy. And once he was sure Jim wasn't going to die where he stood Bones spun Jim to face him. "What the hell were you thinking?" In true Bones fashion he completely ignored the three admirals in the room. "It had to wait." Jim said. "Wait for what? For you to die?" Bones snarled. Jim's eyes turned glacial. "This debrief was important."

"NOT MORE IMPORTANT THAN YOUR LIFE!" Bones roared and it checked Jim for a moment he'd seen Bones in some tempers but this was different. Bones grabbed Jim and looked like he was about to shake him. "I know this mission went to shit. I don't know why and frankly I don't care. I know you did what was right. Because your James Kirk my best friend. And I trust you. And Frankly this was one of those missions that us mere mortals wouldn't have realised there was anything wrong until you were done. But damn it Jim whatever it is it isn't worth dying for!"

This time he did shake Jim. Jim had been staring at Bones with a glacial, blank expression but by the end it had melted into something like disbelief. "You mean that." He whispered. He hated himself for sounding so vulnerable but he couldn't help it. His tone checked Bones from his rant and for the first time Bones really looked at his friend.

"Jim what the fuck happened? Of course I mean that. How could you think I didn't? You asked me to trust you and I do. I always have." With Bones' heart felt admission Jim felt his mask slipping. "You'd be the only one to think that Bones."

"Bullshit." Bones said.

"Jim's right Dr. McCoy." Chris Pike said sitting forward and drawing attention to him. He looked up at Jim. "Spock just sent me his report. It makes for interesting reading." Jim's expression was glacial again.

Chris turned to Bones. "The command crew made their opinions of Jim's choices during the last mission explicit. Jim you didn't tell me they relieved you from duty." Jim's eyes flashed fire. "Yes. Spock is acting captain at the moment."

"And yet you still did exactly what was needed." Admiral Archer and Barnett looked at each other unable to believe it. "Of course I did." Jim said. "You don't know what would have happened if I hadn't. I did what I had to save people."

"But now I have to do it all again. You've seen what will happen if I don't. Admirals please give me a team."

Bones turned Jim to face him again. "Jim what are you doing?" "I'm leaving the Enterprise Bones." Jim said strongly. "The crew don't trust me. Not even my First Officer and I won't work that way." Bones was outraged for a moment. "Spock doesn't trust you Jim you're..." "That doesn't seem to matter." Jim said anguish flashing in his eyes for a moment. "He said it didn't matter. That I'd betrayed you all. That I had betrayed him. He hasn't spoken to me for two weeks. And he's blocked the..." Jim couldn't finish the sentence. The pain was almost crippling.

Bones looked so angry for a moment he looked incapable of speech. "That fucking hobgoblin. He was meant too... He is..." Bones seemed to lose his words. He gave up articulating and pulled Jim into a hug. "Don't put me in the same category as them Jim. It's insulting." For the first time since the mission had begun Jim thought he might survive the clusterfuck.

He looked down and then looked at his friend directly in the eye. "There are things I can't explain but someone fucked up and now everything I did on that mission means nothing. I lost everything and I won't have it be for nothing. I'll put it right if it's the last thing I do."

At that moment Admiral Barnett sat forward. "You have your team Captain but are you sure this is what you-" "No it's not what I want at all." Jim said. "But I have people to protect. That's my job now."

"I don't understand anything other than this," Bones said clasping his hand around Jim's bicep. "Your leaving the Enterprise probably to do something dangerous and I don't trust anyone to keep you safe. The Green- Blooded Hobgoblin was meant to do it but since he's been found wanting, the bastard, it'll have to be me." Bones forced Jim to look at him. "I won't let you do this alone. Not ever."

"Bones..." "No Jim. I'm not leaving you to this on your own. Not this time." "Bones where I'm going it'll be dark." "Been some dark places myself Jim. Trust me I know where you're heading and you'll need a good medic."

"What about your daughter. I can't pull you from her." Jim stared at his friend. He honestly hadn't expected this. He had done what he'd had too but he had thought that he'd lost everyone he'd cared about when he decided what he was going to do. He'd believed that because the people he had thought as friends had told him so. Because the command team, because Spock had looked at him like he was worth nothing. And Jim had believed them. Had accepted the price of doing the right thing.

But now Bones was here. Willing to jump into the flames. Willing to follow Jim into something he had no way of understanding, simply because that was where Jim was going. Jim had never loved his friend more than he had in that moment.

"And how would I ever be able to look my daughter in the face if I left her uncle to rot. If I left my best friend to the dark because he was brave enough to face down a command team and do the right thing." Bones said throwing his arms up in the air.

"You're right Jim there are things I don't understand but there are things I do." He clasped both of Jim's arms. "Come on Jim you're an Empath. Feel what I'm telling you. You know I'm telling you the truth!"

Jim reeled back and stared at Bones like he had a second head. Bones smirked. "Oh yeah Jim I know about that, so use it, and tell me I'm lying to you."

"How...?" Jim shook his head now wasn't the time to be asking those kind of questions. But as soon as he touched Bones he knew he was speaking the truth and Jim felt his resolve weakening.

"How can you trust me?" He asked brokenly. Bones looked at Jim then. "Because in the four years I've known you, you've given me no reason not too. And my whole life you're the only one that has ever stuck with me through trouble. " He said simply. "Besides," He grinned "I'm too old to break in a new best friend so I guess I'm gonna have to follow the idiot that holds the title now. The damn fool is likely to get himself killed otherwise."

Like that the moment was over and Bones was back to the best friend that Jim knew, but he also knew he wouldn't forget the words and neither would Bones let him forget.

Jim took a deep breath and met the faces of the Admirals "I'll take the team but with your permission Sir," He turned his attention to Archer, "I'd like to pick the recruited from anywhere. I already have ideas where I can get the other three from."

Chris Pike sat forward at this. "Dr. McCoy, are you sure your position on the Enterprise as CMO is a respected one." Bones' eyes burned for a moment. "I don't give a damn whether it's respected or not." He said matter of fact. "They hurt my captain. They asked for his trust and betrayed it. More than that they betrayed my best friend. I know what I'm in for." Jim looked at him, "Bones," He whispered.

"I know Jim." Bones said looking at his friend. "I know you never wanted this but this isn't your choice to make. I'm coming with you. Deal with it." Jim stared at Bones and McCoy stared back calmly. Whatever Jim had seen had obviously made up his mind because he said nothing else.

McCoy looked at the Admirals. "How do you want to play this?" Chris sat forward, "Ask your best friend he knows more than anything else what your facing."

Jim looked at the people in the room. "I have to keep them from chasing the Enterprise again. They may hate me, but they're still my crew. I want them safe and as my last act as captain I will make sure they are. I need to draw them off." He stopped talking for a moment and then looked at Chris. "Tell them that I taken by the prisoners. Tell them that while I was transporting the prisoners to the brig they escaped and I was kidnapped in the fire fight. Can you make it look good?"

Archer grinned. "Captain I've been a Black Ops Unit Chief longer than you've been alive I can take anything and make it true." "Then make it look like I was taken. Tell them I was taken and you've got a team looking for me. But you've lost the trail and found blood. More than a person can live without. Then send them to the other side of the quadrant in the opposite direction to where I'm going. I won't have this hurt anyone else." Jim said.

Jim looked at Bones then, "I know you can act Bones but you're gonna have to pull a stellar performance out your hat here. They can't know. They can't guess." Bones grasped his bicep. "Jim I won't have to act, I'm so mad with them that when I tell them all I'm leaving because they fucked up your life and now your in danger I'll be screaming the truth."

Jim looked at his friend then. "You believe that." Bones clasped Jim's shoulder. "I know that."

Jim closed his eyes for a moment. "Okay then. I guess it's time to do this."

The Captain of the Enterprise was about to become no more.


End file.
